|
| Status |
Public on Feb 16, 2021 |
| Title |
MM5_H3K27ac_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
H3K27ac_ChIP-seq
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: newly diagnosed patients with MM
subject id: MM5
cell type: Plasma cells from bone marrow aspirates
chip antibody: anti-H3K27ac (Abcam, ab4729)
|
| Treatment protocol |
TL-Om1 cells were cross-linked with formaldehyde for 10 min. Lysates were clarified from sonicated nuclei and H3K27ac-DNA complexes were isolated with antibody. A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment.
|
| Growth protocol |
Plasma cells were isolated by CD138 immunomagnetic bead selection from bone marrow aspirates of newly diagnosed patients with MM, which were obtained from the National University Hospital after approval by the institutional ethical committee.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction from the H3K27ac ChIP-seq samples and sequencing of single-end 50bps long reads by the Illumina HiSeq 4000 were performed at BGI Biotech Solutions Co. Ltd (Hong Kong, China).
Single end ChIP-Seq sequencing
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
bone marrow of newly diagnosed patients with MM
|
| Data processing |
ChIP-seq reads were mapped to human hg19 reference genome using bowtie2 program with default parameters.
Aligned ChIP-seq reads were remove duplicate with samtools rmdup package.
ChIP-Seq peaks were called with MACS2 software, version 2.1.1.2016030. Threshold for the peaks called is q-value < 0.01, keep-dup=1
Genome_build: hg19
Supplementary_files_format_and_content: broadPeak files called with MACS2
|
| |
|
| Submission date |
Feb 25, 2020 |
| Last update date |
Feb 16, 2021 |
| Contact name |
Tze King Tan |
| Organization name |
National University of Singapore
|
| Department |
Cancer Science Institute
|
| Lab |
Takaomi Sanda Lab
|
| Street address |
14 Medical Drive
|
| City |
Singapore |
| ZIP/Postal code |
117599 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE145891 |
H3K27ac ChIP-seq for primary multiple myeloma patients’ samples (MM1-MM10) |
| GSE145938 |
Super-enhancer profiling combined with CDK7 inhibition-transcripts identifies novel oncogenes of multiple myeloma. |
|
| Relations |
| BioSample |
SAMN14206187 |
| SRA |
SRX7798977 |
